bf62c01cee8dc176445aa131e2fd6ea847a4eb68
lrnassar
  Thu May 28 11:32:52 2026 -0700
Adding UMD TP53 variant track (umdTp53) on hg19 and hg38 under a new Locus-Specific superTrack. refs #37648

Shows variants from the UMD TP53 database (p53.fr, Soussi & Leroy) as a
bigBed 9+, one row per unique TP53 variant. Coloured by curator pathogenicity
classification. Filters: pathogenicity, variantClassification, variantType,
tumor frequency. Search by HGVS cDNA name and canonical protein change via
extraIndex + trix. Linkouts to COSMIC and dbSNP.

Otto pipeline polls p53.fr weekly; rebuilds only when the upstream zips
actually change. Cron-silent on no-op so unchanged weeks don't email.

Adds src/hg/utils/otto/umdTp53/ (build scripts + parser + .as schema),
src/hg/makeDb/trackDb/human/umdTp53.ra (track stanza),
src/hg/makeDb/trackDb/human/umdTp53.html (description page),
src/hg/makeDb/trackDb/human/locusSpec.ra (shared superTrack definition).

Includes locusSpec.ra and umdTp53.ra from human/trackDb.ra (alpha-gated).
Adds include of ../locusSpec.ra to human/hs1/trackDb.ra so the strict
trackDb checker resolves the parent in the same include chain as the
existing mucins children. Drops the redundant locusSpec stanza from
human/mucins.ra now that it lives in its own file.

diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra
index 174cba0a381..00cd7a137ee 100644
--- src/hg/makeDb/trackDb/human/trackDb.ra
+++ src/hg/makeDb/trackDb/human/trackDb.ra
@@ -5627,15 +5627,18 @@
 include g2p.ra
 include varFreqs.ra alpha,beta
 include phasedVars.ra
 
 track dnaMethylation
 superTrack on
 shortLabel DNA Methylation
 longLabel DNA Methylation
 group regulation
 priority 3
 pennantIcon New red ../goldenPath/newsarch.html#031626 "Released Mar. 16, 2026"
 html dnaMethylation.html
 
 include methylationAtlas.ra
 include methylationAtlasSignals.ra
+
+include locusSpec.ra alpha
+include umdTp53.ra alpha